in length. Thus, in a GWAS that examines 300,000 SNP markers, these shared stretches will typically include 10 – 20 genotyped markers. When there is ambiguity about which haplotype stretch should be “copied” to fill in missing genotypes for a particular individual, imputation programs typically provide an answer that summarizes this ambiguity (for example, in 60% of reconstructions genotype A/A was observed at a specific site, whereas in the remaining 40% a different genotype A/C was observed).
